Job ID = 6627191 SRX = SRX8521315 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:31:16 prefetch.2.10.7: 1) Downloading 'SRR11978741'... 2020-07-14T01:31:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:32:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:32:20 prefetch.2.10.7: 'SRR11978741' is valid 2020-07-14T01:32:20 prefetch.2.10.7: 1) 'SRR11978741' was downloaded successfully 2020-07-14T01:32:20 prefetch.2.10.7: 'SRR11978741' has 0 unresolved dependencies Read 7594195 spots for SRR11978741/SRR11978741.sra Written 7594195 spots for SRR11978741/SRR11978741.sra 2020-07-14T01:32:57 prefetch.2.10.7: 1) Downloading 'SRR11978742'... 2020-07-14T01:32:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:20 prefetch.2.10.7: 'SRR11978742' is valid 2020-07-14T01:34:20 prefetch.2.10.7: 1) 'SRR11978742' was downloaded successfully 2020-07-14T01:34:20 prefetch.2.10.7: 'SRR11978742' has 0 unresolved dependencies Read 7427614 spots for SRR11978742/SRR11978742.sra Written 7427614 spots for SRR11978742/SRR11978742.sra 2020-07-14T01:34:58 prefetch.2.10.7: 1) Downloading 'SRR11978743'... 2020-07-14T01:34:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:20 prefetch.2.10.7: 'SRR11978743' is valid 2020-07-14T01:36:20 prefetch.2.10.7: 1) 'SRR11978743' was downloaded successfully 2020-07-14T01:36:20 prefetch.2.10.7: 'SRR11978743' has 0 unresolved dependencies Read 7776600 spots for SRR11978743/SRR11978743.sra Written 7776600 spots for SRR11978743/SRR11978743.sra 2020-07-14T01:36:55 prefetch.2.10.7: 1) Downloading 'SRR11978744'... 2020-07-14T01:36:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:37:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:37:53 prefetch.2.10.7: 'SRR11978744' is valid 2020-07-14T01:37:53 prefetch.2.10.7: 1) 'SRR11978744' was downloaded successfully 2020-07-14T01:37:53 prefetch.2.10.7: 'SRR11978744' has 0 unresolved dependencies Read 7627111 spots for SRR11978744/SRR11978744.sra Written 7627111 spots for SRR11978744/SRR11978744.sra 2020-07-14T01:38:33 prefetch.2.10.7: 1) Downloading 'SRR11978745'... 2020-07-14T01:38:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:39:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:39:08 prefetch.2.10.7: 'SRR11978745' is valid 2020-07-14T01:39:08 prefetch.2.10.7: 1) 'SRR11978745' was downloaded successfully 2020-07-14T01:39:08 prefetch.2.10.7: 'SRR11978745' has 0 unresolved dependencies Read 3094225 spots for SRR11978745/SRR11978745.sra Written 3094225 spots for SRR11978745/SRR11978745.sra 2020-07-14T01:39:33 prefetch.2.10.7: 1) Downloading 'SRR11978746'... 2020-07-14T01:39:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:07 prefetch.2.10.7: 'SRR11978746' is valid 2020-07-14T01:40:07 prefetch.2.10.7: 1) 'SRR11978746' was downloaded successfully 2020-07-14T01:40:07 prefetch.2.10.7: 'SRR11978746' has 0 unresolved dependencies Read 2981867 spots for SRR11978746/SRR11978746.sra Written 2981867 spots for SRR11978746/SRR11978746.sra 2020-07-14T01:40:34 prefetch.2.10.7: 1) Downloading 'SRR11978747'... 2020-07-14T01:40:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:41:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:41:04 prefetch.2.10.7: 'SRR11978747' is valid 2020-07-14T01:41:04 prefetch.2.10.7: 1) 'SRR11978747' was downloaded successfully 2020-07-14T01:41:04 prefetch.2.10.7: 'SRR11978747' has 0 unresolved dependencies Read 3175833 spots for SRR11978747/SRR11978747.sra Written 3175833 spots for SRR11978747/SRR11978747.sra 2020-07-14T01:41:29 prefetch.2.10.7: 1) Downloading 'SRR11978748'... 2020-07-14T01:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:16 prefetch.2.10.7: 'SRR11978748' is valid 2020-07-14T01:42:16 prefetch.2.10.7: 1) 'SRR11978748' was downloaded successfully 2020-07-14T01:42:16 prefetch.2.10.7: 'SRR11978748' has 0 unresolved dependencies Read 3117765 spots for SRR11978748/SRR11978748.sra Written 3117765 spots for SRR11978748/SRR11978748.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627449 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:20 42795210 reads; of these: 42795210 (100.00%) were unpaired; of these: 37369916 (87.32%) aligned 0 times 4061290 (9.49%) aligned exactly 1 time 1364004 (3.19%) aligned >1 times 12.68% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1092991 / 5425294 = 0.2015 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:52:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 10:52:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:35: 1000000 INFO @ Tue, 14 Jul 2020 10:52:43: 2000000 INFO @ Tue, 14 Jul 2020 10:52:51: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 10:52:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:00: 4000000 INFO @ Tue, 14 Jul 2020 10:53:03: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:53:03: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:53:03: #1 total tags in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:53:03: #1 tags after filtering in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:03: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:03: #2 number of paired peaks: 384 WARNING @ Tue, 14 Jul 2020 10:53:03: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:03: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:03: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:03: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:03: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:03: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:53:03: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05_model.r WARNING @ Tue, 14 Jul 2020 10:53:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:53:03: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:53:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:53:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:53:05: 1000000 INFO @ Tue, 14 Jul 2020 10:53:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:14: 2000000 INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.05_summits.bed INFO @ Tue, 14 Jul 2020 10:53:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:53:22: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 10:53:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:31: 4000000 INFO @ Tue, 14 Jul 2020 10:53:34: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:53:34: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:53:34: #1 total tags in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:53:34: #1 tags after filtering in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:34: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:34: #2 number of paired peaks: 384 WARNING @ Tue, 14 Jul 2020 10:53:34: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:34: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:34: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:34: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:34: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:34: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:53:34: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10_model.r WARNING @ Tue, 14 Jul 2020 10:53:34: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:53:34: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:53:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:53:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:53:35: 1000000 INFO @ Tue, 14 Jul 2020 10:53:42: 2000000 INFO @ Tue, 14 Jul 2020 10:53:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:49: 3000000 INFO @ Tue, 14 Jul 2020 10:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.10_summits.bed INFO @ Tue, 14 Jul 2020 10:53:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:53:57: 4000000 INFO @ Tue, 14 Jul 2020 10:53:59: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:53:59: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:53:59: #1 total tags in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:53:59: #1 tags after filtering in treatment: 4332303 INFO @ Tue, 14 Jul 2020 10:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:59: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:59: #2 number of paired peaks: 384 WARNING @ Tue, 14 Jul 2020 10:53:59: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:59: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:59: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:59: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:59: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:59: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:53:59: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20_model.r WARNING @ Tue, 14 Jul 2020 10:53:59: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:53:59: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:53:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:53:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521315/SRX8521315.20_summits.bed INFO @ Tue, 14 Jul 2020 10:54:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 1 millis CompletedMACS2peakCalling